Update export vcf - Githubissues

maize-genetics / phg_v2

Practical Haplotype Graph (PHG) version 2

Apache License 2.0

21 stars 2 forks source link

Description

Changed imputation documentation to use export-vcf --sample-file instead of --sample-names. Changed export-vcf parameter --outputDir to --output-dir Added list-samples step to imputation documentation

Type of change

What type of changes does your code introduce? Put an x in boxes that apply.

[ ] CHANGE (fix or feature that would cause existing functionality to not work as expected)
[ ] FEATURE (non-breaking change which adds functionality)
[ ] BUGFIX (non-breaking change which fixes an issue)
[X] ENHANCEMENT (non-breaking change which improves existing functionality)
[ ] NONE (if none of the other choices apply. Example, tooling, build system, CI, docs, etc.)

Checklist:

[ ] I have performed a self-review of my code
[ ] I have commented my code, particularly in hard-to-understand areas
[ ] I have updated relevant documentation

Changelog entry

Please add a one-line changelog entry below. This will be copied to the changelog file during the release process.

Improved imputation documentation

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 82.84%. Comparing base (9f75594) to head (0e20f24). Report is 7 commits behind head on main.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #225 +/- ## ======================================= Coverage 82.84% 82.84% ======================================= Files 78 78 Lines 5112 5112 Branches 850 850 ======================================= Hits 4235 4235 Misses 560 560 Partials 317 317 ``` | [Flag](https://app.codecov.io/gh/maize-genetics/phg_v2/pull/225/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=maize-genetics) | Coverage Δ | | |---|---|---| | [](https://app.codecov.io/gh/maize-genetics/phg_v2/pull/225/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=maize-genetics) | `82.84% <100.00%> (ø)` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=maize-genetics#carryforward-flags-in-the-pull-request-comment) to find out more.